[R-sig-Fedora] problems compiling packages | 3.3.0 | Linux

Gordon Ball
Thu, 09 Jun 2016 12:06:38 -0000

Brian Fallik <brian at ...> writes:

>
> Hi Tom,
>
> I'm seeing another similar build failure with the recent 3.3.0-5 and
I'm a
> bit stumped about what's going on.
>
> On a fresh VM, after installing 3.3.0-5 and then running:
>   install.packages(c("lpSolveAPI), method="curl",
repos="
> https://cran.rstudio.com")
> the build fails with:
>   gcc: /builddir/build/BUILD/R-3.3.0/zlib-1.2.8/target/usr/lib64/libz.a: No
> such file or directory
>   gcc: /builddir/build/BUILD/R-3.3.0/bzip2-1.0.6/target/usr/lib64/libbz2.a:
> No such file or directory
>   gcc: /builddir/build/BUILD/R-3.3.0/xz-5.2.2/target/usr/lib64/liblzma.a:
> No such file or directory
>   gcc: /builddir/build/BUILD/R-3.3.0/pcre-8.38/target/usr/lib64/libpcre.a:
> No such file or directory
>   gcc:
> /builddir/build/BUILD/R-3.3.0/curl-7.48.0/target/usr/lib64/libcurl.a: No
> such file or directory



I also noticed this today (doing a large rebuild upgrading to bioconductor 3.3).

The culprit appears to be that FLIBS in /usr/lib64/R/etc/Makeconf (line 43)
still references these paths, and hence presumably it is only triggered if
you compile a package containing fortran code.

Deleting the paths from Makeconf makes the error go away (although I'm not
certain whether this means the correct libraries are being linked against -
this might be storing up problems for the future).

Gordon

(Centos 6.8, R 3.3.0-5)